Gene-chip technology and its applications

Gene Chips are finding extensive use in animal and plant science. Generally microarrays are of two kind, cDNA or oligonucleotide. cDNA microarrays were developed at Stanford University, whereas oligonucleotide were developed by Affymetrix. The construction of cDNA or oligonucleotide on a glass slide helps to compare the gene expression level of treated and control samples by labeling mRNA with green (Cy3) and red (Cy5) dyes. The hybridized gene chip emit fluorescence whose intensity and colour can be measured. RNA labeling can be done directly or indirectly. Indirect method involves amino allyle modified dUTP instead of pre-labelled nucleotide. Hybridization of gene chip generally occurs in a minimum volume possible and to ensure the hetroduplex formation, a ten fold more DNA is spotted on slide than in the solutions. A confocal or semi confocal laser technologies coupled with CCD camera are used for image acquisition. For standardization, house keeping genes are used or cDNA are spotted in gene chip that are not present in treated or control samples. Moreover, statistical analysis (image analysis) and cluster analysis softwares have been developed by Stanford University. The gene-chip technology has many applications like expression analysis, gene expression signatures (molecular phenotypes) and promoter regulatory element co-expression.

Value management and post-occupancy evaluation: closing the loop

This paper considers the relationship between value management and facilities management. The findings are particularly relevant to large client organisations which procure new buildings on a regular basis. It is argued that the maximum effectiveness of value management can only be achieved if it is used in conjunction with an ongoing commitment to post-occupancy evaluation. SMART value management is seen to provide the means of ensuring that an individual building design is in alignment with the client’s strategic property needs. However, it is also necessary to recognise that an organisation’s strategic property needs will continually be in a state of change. Consequentially, economic and functional under-performance can only be avoided by a regular performance audit of existing property stock in accordance with changing requirements. Such a policy will ensure ongoing competitiveness through organisational learning. While post-occupancy evaluation represents an obvious additional service to be provided by value management consultants, it is vital that the necessary additional skills are acquired. Process management skills and social science research techniques are clearly important. However, there is also a need to improve mechanisms for data manipulation. Success can only be achieved if equal attention is given to issues of process, structure and content.

Effect of water-soluble polymers, polyethylene glycol and poly(vinylpyrrolidone),on the gelation of aqueous micellar solutions of Pluronic copolymer F127

The micellization of F127 (E98P67E98) in dilute aqueous solutions of polyethylene glycol (PEG6000 and PEG35000) and poly(vinylpyrrolidone) (PVP K30 and PVP K90) is studied. The average hydrodynamic radius (rh,app) obtained from the dynamic light scattering technique increased with increase in PEG concentration but decreased on addition of PVP, results which are consistent with interaction of the micelles with PEG and the formation of micelles clusters, but no such interaction occurs with PVP. Tube inversion was used to determine the onset of gelation. The critical concentration of F127 for gelation increased on addition of PEG and of PVP K30 but decreased on addition of PVP K90. Small-angle X-ray scattering (SAXS) was used to show that the 30 wt% F127 gel structure (fcc) was independent of polymer type and concentration, as was the d-spacing and so the micelle hard-sphere radius. The maximum elastic modulus (G0 max) of 30 wt% F127 decreased from its value for water alone as PEG was added, but was little changed by adding PVP. These results are consistent with the packed-micelles in the 30 wt% F127 gel being effectively isolated from the polymer solution on the microscale while, especially for the PEG, being mixed on the macroscale.

Everything and nothing project

An EPRSC ‘Partnerships for Public Engagement’ scheme 2010. FEC 122,545.56/UoR 10K everything and nothing is a performance and workshop which engages the public creatively with mathematical concepts: the Poincare conjecture, the shape of the universe, topology, and the nature of infinity are explored through an original, thought provoking piece of music theatre. Jorge Luis Borges' short story 'The Library of Babel' and the aviator Amelia Earhart’s attempt to circumnavigate the globe combine to communicate to audience key mathematical concepts of Poincare’s conjecture. The project builds on a 2008 EPSRC early development project (EP/G001650/1) and is led by an interdisciplinary team the19thstep consisting of composer Dorothy Ker, sculptor Kate Allen and mathematician Marcus du Sautoy. everything and nothing has been devised by Dorothy Ker and Kate Allen, is performed by percussionist Chris Brannick, mezzo soprano Lucy Stevens and sound designer Kelcey Swain. The UK tour targets arts-going audiences, from the Green Man Festival to the British Science Festival. Each performance is accompanied with a workshop led by Topologist Katie Steckles. Alongside the performances and workshops is a website, http://www.everythingandnothingproject.com/ The Public engagement evaluation and monitoring for the project are carried out by evaluator Bea Jefferson. The project is significant in its timely relation to contemporary mathematics and arts-science themes delivering an extensive programme of public engagement.

Coping with delays for real-time gaze control (The Fall and Rise of the Smiths Regulator)

In this paper we describe how to cope with the delays inherent in a real time control system for a steerable stereo head/eye platform. A purposive and reactive system requires the use of fast vision algorithms to provide the controller with the error signals to drive the platform. The time-critical implementation of these algorithms is necessary, not only to enable short latency reaction to real world events, but also to provide sufficiently high frequency results with small enough delays that controller remain stable. However, even with precise knowledge of that delay, nonlinearities in the plant make modelling of that plant impossible, thus precluding the use of a Smith Regulator. Moreover, the major delay in the system is in the feedback (image capture and vision processing) rather than feed forward (controller) loop. Delays ranging between 40msecs and 80msecs are common for the simple 2D processes, but might extend to several hundred milliseconds for more sophisticated 3D processes. The strategy presented gives precise control over the gaze direction of the cameras despite the lack of a priori knowledge of the delays involved. The resulting controller is shown to have a similar structure to the Smith Regulator, but with essential modifications.

Wind observations above an urban river using a new lidar technique, scintillometry and anemometry

Flow along rivers, an integral part of many cities, might provide a key mechanism for ventilation – which is important for air quality and heat stress. Since the flow varies in space and time around rivers, there is limited utility in point measurements. Ground-based remote sensing offers the opportunity to study 3D flow in locations which are hard to observe. For three months in the winter and spring of 2011, the atmospheric flow above the River Thames in central London was observed using a scanning Doppler lidar, a dual-beam scintillometer and sonic anemometry. First, an inter-comparison showed that lidar-derived mean wind-speed estimates compare almost as well to sonic anemometers (root-mean-square error (rmse) 0.65–0.68 m s–1) as comparisons between sonic anemometers (0.35–0.73 m s–1). Second, the lidar duo-beam scanning strategy provided horizontal transects of wind vectors comparison with scintillometer rmse 1.12–1.63 m s–1) which revealed mean and turbulent flow across the river and surrounds; in particular: chanelling flow along the river and turbulence changes consistent with the roughness changes between built to river environments. The results have important consequences for air quality and dispersion around urban rivers, especially given that many cities have high traffic rates on bankside roads.

Exposure to fine particulate matter in ten night clubs in Athens Greece: studying the effect of ventilation, cigarette smoking and resuspension

The aim of the present work is to study the occupants' exposure to fine particulate concentrations in ten nightclubs (NCs) in Athens, Greece. Measurements of PM1 and PM 2.5 were made in the outdoor and indoor environment of each NC. The average indoorPM1 andPM 2.5 concentrations were found to be 181.77 μgm−3 and 454.08 μg m−3 respectively, while the corresponding outdoor values were 11.04 μg m−3 and 32.19 μg m−3. Ventilation and resuspension rates were estimated through consecutive numerical experiments with an indoor air quality model and were found to be remarkably lower than the minimum values recommended by national standards. The relative effects of the ventilation and smoking on the occupants' exposures were examined using multiple regression techniques. Itwas found that given the low ventilation rates, the effect of smoking as well as the occupancy is of the highest importance. Numerical evaluations showed that if the ventilation rates were at the minimum values set by national standards, then the indoor exposures would be reduced at the 70% of the present exposure values.

Formal theory building for the avalanche game: explaining counter-intuitive behaviour of a complex system using geometrical and human behavioural/physiological effects

In 'Avalanche', an object is lowered, players staying in contact throughout. Normally the task is easily accomplished. However, with larger groups counter-intuitive behaviours appear. The paper proposes a formal theory for the underlying causal mechanisms. The aim is to not only provide an explicit, testable hypothesis for the source of the observed modes of behaviour-but also to exemplify the contribution that formal theory building can make to understanding complex social phenomena. Mapping reveals the importance of geometry to the Avalanche game; each player has a pair of balancing loops, one involved in lowering the object, the other ensuring contact. For more players, sets of balancing loops interact and these can allow dominance by reinforcing loops, causing the system to chase upwards towards an ever-increasing goal. However, a series of other effects concerning human physiology and behaviour (HPB) is posited as playing a role. The hypothesis is therefore rigorously tested using simulation. For simplicity a 'One Degree of Freedom' case is examined, allowing all of the effects to be included whilst rendering the analysis more transparent. Formulation and experimentation with the model gives insight into the behaviours. Multi-dimensional rate/level analysis indicates that there is only a narrow region in which the system is able to move downwards. Model runs reproduce the single 'desired' mode of behaviour and all three of the observed 'problematic' ones. Sensitivity analysis gives further insight into the system's modes and their causes. Behaviour is seen to arise only when the geometric effects apply (number of players greater than degrees of freedom of object) in combination with a range of HPB effects. An analogy exists between the co-operative behaviour required here and various examples: conflicting strategic objectives in organizations; Prisoners' Dilemma and integrated bargaining situations. Additionally, the game may be relatable in more direct algebraic terms to situations involving companies in which the resulting behaviours are mediated by market regulations. Finally, comment is offered on the inadequacy of some forms of theory building and the case is made for formal theory building involving the use of models, analysis and plausible explanations to create deep understanding of social phenomena.

Theory building with system dynamics: topic and research contributions

The article discusses various reports published within the issue, including the articles "Closing the Loop: Promoting Synergies with other Theory Building Approaches to Improve System Dynamics Practice," by Birgit Kopainsky and Luis Luna-Reyes, and "On improving dynamic decision-making: Implications from multiple-process cognitive theory," by Bent Bakken.

Predicting the risks from climate change to forage and crop production for animal feed

Climate change is expected to bring warmer temperatures, changes to rainfall patterns, and increased frequency of extreme weather. Projections of climate impacts on feed crops show that there will likely be opportunities for increased productivity as well as considerable threats to crop productivity in different parts of the world over the next 20 to 50 years. On balance, we anticipate substantial risks to the volume, volatility, and quality of animal feed supply chains from climate change. Adaptation strategies and investment informed by high quality research at the interface of crop and animal science will be needed, both to respond to climate change and to meet the increasing demand for animal products expected over the coming decades.

Synergetic effect of carbon nanopore size and surface oxidation on CO2 capture from CO2/CH4 mixtures

We have studied the synergetic effect of confinement (carbon nanopore size) and surface chemistry (the number of carbonyl groups) on CO2 capture from its mixtures with CH4 at typical operating conditions for industrial adsorptive separation (298 K and compressed CO2CH4 mixtures). Although both confinement and surface oxidation have an impact on the efficiency of CO2/CH4 adsorptive separation at thermodynamics equilibrium, we show that surface functionalization is the most important factor in designing an efficient adsorbent for CO2 capture. Systematic Monte Carlo simulations revealed that adsorption of CH4 either pure or mixed with CO2 on oxidized nanoporous carbons is only slightly increased by the presence of functional groups (surface dipoles). In contrast, adsorption of CO2 is very sensitive to the number of carbonyl groups, which can be examined by a strong electric quadrupolar moment of CO2. Interestingly, the adsorbed amount of CH4 is strongly affected by the presence of the co-adsorbed CO2. In contrast, the CO2 uptake does not depend on the molar ratio of CH4 in the bulk mixture. The optimal carbonaceous porous adsorbent used for CO2 capture near ambient conditions should consist of narrow carbon nanopores with oxidized pore walls. Furthermore, the equilibrium separation factor was the greatest for CO2/CH4 mixtures with a low CO2 concentration. The maximum equilibrium separation factor of CO2 over CH4 of ∼18–20 is theoretically predicted for strongly oxidized nanoporous carbons. Our findings call for a review of the standard uncharged model of carbonaceous materials used for the modeling of the adsorption separation processes of gas mixtures containing CO2 (and other molecules with strong electric quadrupolar moment or dipole moment).